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Ideas

Sabrina appearance or mention
Zapdos grabs them at the end of the Conference, right before Officer Jenny gets them.
Team Rocket attacks Scott and Jill.
Jessie and James cameo appearance.
Squirtle learns Hydro Pump in the end.
Mewtwo's goal is to clone every Pokemon in the world so that he won't be alone.
Team Rocket members begin capturing the cloned Pokemon as Giovanni tries captuing Mewtwo. Scott saves some of them, but they begin attacking him anyway.
Giovanni captures Mewtwo with the Masterball stolen from the Pokemon Ressurection Center, but once he released Mewtwo from its ball, Mewtwo destroys the ball with his Psychic powers.
The whole arc is either 1-3 episodes.
Mewtwo eventually captures the Team Rocket members, and he is now the villian. Scott and Jill work with Butch, Cassidy and Scout to help free them all.
Mewtwo clones all of their Pokemon, and eventually clones Articuno and Moltres and sends them to attack Zapdos, and they eventaully do.
Jill tells Mewtwo that if he is trying to repopulate the world with his clones, then it'll take much more because theres a bunch more Pokemon in the Johto Region. Mewtwo then puts them outside the cloning chamber to watch him begin to clone Giovanni as he was, asking him how he likes having his body horrifically altered and DNA changing
Mew reveals itself, previously transformed as one of the clones, and helps free Scott and Jill, and they help free everyone else and their Pokemon, as Mewtwo begins trying to clone HUMANS as well.
Jill tells Scott to send his Farfetch'd to fly away and get help, and he writes a note and ties it to Farfetch'd feet.
Mew begins turning into Dark-typed Pokemon from Johto and is immune to Mewtwo's Psychic abilities.
(Insert Stuff)
In the end, Officer Jenny, Prof. Oak and the Pokemon Ressurection Crew come over by helicopter, and Prof. Oak says he will take the Pokemon back to his lab and teach them to be nice and learn the greatness of Pokemon. Offficer Jenny takes Jill and Scott back home, where his mother is waiting.

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